Ben Watson scored with his first touch, from the penalty spot, after coming on as a substitute to snatch a dramatic, late equaliser for 10-man Wigan.
Hugo Rodallega had crossed for Victor Moses to tuck in the opener for Wigan.
Stoke made it 1-1 when Gary Caldwell was sent off for handball, leading to a penalty scored by Jon Walters.
Then came a thrilling finish as Cameron Jerome fired Stoke ahead before Watson rescued a draw after Ryan Shotton pulled Rodallega's shirt.
The final penalty incident was a controversial one by referee Michael Oliver as Rodallega went down easily following just the slightest of tugs by Shotton. Set-piece specialist Watson was brought on specifically to take the kick and did not disappoint.
Earlier, the first half had been an open and high-tempo affair, not living up to this fixture's image. Stoke had looked the better side in the early stages but then the visitors struck with a swift, counter-attacking move just before the break.
Stoke were struggling to create chances - other than from set-pieces - but the game changed as Caldwell was rightly dismissed for blocking Jerome's header at goal.
Soon afterwards, Stoke were 2-1 ahead - rather undeserved on the balance of play - but Wigan had the final say.
The point moved Roberto Martinez's visitors to within two points of fourth-bottom QPR. Wigan, in 18th spot, are a point clear of Blackburn and two ahead of Bolton.
There had been an early scare for Wigan as the ball struck defender Caldwell's arm in the area as he tussled with Peter Crouch but no penalty was awarded.
Stoke used their power at dead-ball situations to try to pressurise Wigan early on, with Robert Huth heading wide from close range after a Rory Delap throw-in.
Ronnie Stam injected some life into Wigan's play by cutting in from the right and striking from 25 yards, forcing Thomas Sorensen to tip over the bar. Rodallega then came close, attempting a lob that the Stoke keeper could not reach but Ryan Shawcross raced back and scrambled clear.
Amusingly, Maynor Figueroa attempted a repeat of his halfway line goal at this ground, when he chipped Thomas Sorensen, but this time his shot ended up well wide of the target.
Wigan made the breakthrough when Stam threaded the ball out to Rodallega who crossed first-time from the right, presenting Moses with the chance to strike into the roof of the net.
After the break, set-pieces continued to look Stoke's main threat. Another Delap throw-in was met by a firm header by Robert Huth, but the ball struck the inside of a post.
They were reinvigorated though as Caldwell was shown his straight red card for handling Jerome's header, after Peter Crouch nodded the ball on. Walters struck low and confidently from the spot, starting an exciting final period of the contest.
Stoke quickly took advantage of their numerical advantage to go 2-1 up as Crouch controlled the ball brilliantly before flicking it forward for Walters. The Stoke striker then nudged the ball to Jerome, who finished with an angled strike into the far corner.
But the debatable penalty decision meant that Wigan salvaged a draw as Shotton was punished and Watson held his nerve, sending Sorensen the wrong way.
Stoke manager Tony Pulis: "It's disappointing for us. I think it's a soft penalty. [Hugo] Rodallega actually pushes Ryan [Shotton] to start with.
"I thought in the first 20-25 minutes we had loads of opportunities. The quality just wasn't as good as it could have been.
"From when we scored our first goal, I thought there was only one winner. But Wigan have become a bit of a bogey side."
Wigan manager Roberto Martinez: "We showed unbelievable character. We defended really well and then, to go down to 10 men and get back to level terms, was the least we deserved.
"It's one of the toughest places to come and referee. They put pressure on you. But the key decisions were right - they were clearly both penalties.
"Ben Watson is mentally strong. He was ready and he was fresh. I had no doubts he was the right man to take that penalty."